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-   -   error while running mpirun command in openfoam (https://www.cfd-online.com/Forums/openfoam-solving/185541-error-while-running-mpirun-command-openfoam.html)

tarunw March 28, 2017 07:27
error while running mpirun command in openfoam
 
I am getting following error message while running mpirun command on a server

Code:
It looks like opal_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during opal_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  opal_shmem_base_select failed
  --> Returned value -1 instead of OPAL_SUCCESS
This message appears only when I am running the code in parallel. How to rectify this problem?
Note: I installed OF-3.0.1 on the server from source code

wyldckat April 30, 2017 12:39
Quick answer/question: Have you managed to solve this problem? I only saw your post today.

If not yet, the problem is likely because the wrong MPI toolbox is being used, specifically the mpirun version being used.

If you Google for the following sentence:
Code:
site:cfd-online.com "wyldckat" "OPAL_SUCCESS"
you should find several situations similar to yours and solutions that worked for others.

tarunw June 3, 2017 18:26
Quote:
Originally Posted by wyldckat (Post 647125)
Quick answer/question: Have you managed to solve this problem? I only saw your post today.

If not yet, the problem is likely because the wrong MPI toolbox is being used, specifically the mpirun version being used.

If you Google for the following sentence:
Code:
site:cfd-online.com "wyldckat" "OPAL_SUCCESS"
you should find several situations similar to yours and solutions that worked for others.
hi bruno
Sorry for the late reply. I tried my best to rectify the situation with the help of the forum but unable to solve the problem.

mpirun version used is openmpi-1.10.0. OF version-3.0.1 and OS on cluster is CentOS 6.7. I have compressed installed OF and thirdParty folders and am sending you the google drive link to that file in a PM. Please have a look at my problem. I request you to please help me as soon as you can (I have to run cases for my thesis and not much time left!!). Eagerly waiting for your reply.

Thanks & Regards
Tarun

wyldckat June 4, 2017 20:13
Hi Tarun,

Many thanks for sharing your whole installation! I've tested it in a VM with CentOS 6.8 and was able to reproduce the problem.

Furthermore, I've finally figured out how to solve the problem. If you run the following command before trying to run mpirun:
Code:
export OPAL_LIBDIR=$OPAL_PREFIX/lib64/
you should no longer get that error message.

If this solves the problem, then:
  1. Edit the file "$HOME/OpenFOAM/OpenFOAM-3.0.1/etc/config/settings.sh".
  2. Look for these lines:
    Code:
    OPENMPI)
        export FOAM_MPI=openmpi-1.10.0
        # Optional configuration tweaks:
        _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config/openmpi.sh`

        export MPI_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$FOAM_MPI

        # Tell OpenMPI where to find its install directory
        export OPAL_PREFIX=$MPI_ARCH_PATH
  3. Add after the line with "OPAL_PREFIX" the new line for "OPAL_LIBDIR", so that those two lines looks like this:
    Code:
        export OPAL_PREFIX=$MPI_ARCH_PATH
        export OPAL_LIBDIR=$OPAL_PREFIX/lib64/
  4. Save and close the file.
  5. Next time you start a new terminal window/tab and/or active this OpenFOAM 3.0.1 environment, it should work as intended.


Curiously enough, I had spotted this issue back in 2013: https://www.cfd-online.com/Forums/op...tml#post457794

Best regards,
Bruno

gamemakerh February 12, 2018 08:58
Thank you Bruno !


On one machine I had problem, solution you described, but on another machine I'm getting way different problem...

I want to use same case but I'm getting error message.

Code:
mpirun has detected an attempt to run as root.
Running at root is *strongly* discouraged as any mistake (e.g., in
defining TMPDIR) or bug can result in catastrophic damage to the OS
file system, leaving your system in an unusable state.

You can override this protection by adding the --allow-run-as-root
option to your cmd line. However, we reiterate our strong advice
against doing so - please do so at your own risk.
The main issue (this is my initial guess) is that I'm using Ubuntu server.

every time I want to launch OpenFOAM I gave to call ./startOpenFOAM command. after this I cant use any mpirun commands.

My workflow is showed below

Code:
0. gmsh file.geo -3 -o file.msh
1. gmshToFoam file.msh
2. changeDirectory
3. decomposePar
4. mpirun -np 4 buoyantBoussinesqSimpleFoam -parallel
5. reconstructPar -latesttime
6. rm -r proc*
Looking forward for any ideas or reference links. Thank you in advance.

Veronicapa February 13, 2018 05:15
mpirun not found
 
Hey

I am a beginner user of OpenFOAM yet. I am trying to run the snappyHexMesh in parallel, but this error comes out:

$ mpirun -np 4 snappyHeymesh -overwrite -parallel
-bash: mpirun: command not found

If anyone can give me advise how to run it in parallel or what is the issue, i will appreciate.

Thanks

rajan19us February 14, 2018 08:03
Seriously?? are you really using 'snappyHeymesh' instead of 'SnappyHexMesh' ??

rmaries March 10, 2019 15:40
mpirun has attempted to run as root.
 
Hi,


I too got this problem in my ubuntu machine. Any one have solution?


I have installed openfoam-1812 using docker in my ubuntu. I am getting this problem.



Thanks in advanc



Quote:
Originally Posted by gamemakerh (Post 681238)
Thank you Bruno !


On one machine I had problem, solution you described, but on another machine I'm getting way different problem...

I want to use same case but I'm getting error message.

Code:
mpirun has detected an attempt to run as root.
Running at root is *strongly* discouraged as any mistake (e.g., in
defining TMPDIR) or bug can result in catastrophic damage to the OS
file system, leaving your system in an unusable state.

You can override this protection by adding the --allow-run-as-root
option to your cmd line. However, we reiterate our strong advice
against doing so - please do so at your own risk.
The main issue (this is my initial guess) is that I'm using Ubuntu server.

every time I want to launch OpenFOAM I gave to call ./startOpenFOAM command. after this I cant use any mpirun commands.

My workflow is showed below

Code:
0. gmsh file.geo -3 -o file.msh
1. gmshToFoam file.msh
2. changeDirectory
3. decomposePar
4. mpirun -np 4 buoyantBoussinesqSimpleFoam -parallel
5. reconstructPar -latesttime
6. rm -r proc*
Looking forward for any ideas or reference links. Thank you in advance.

Marina PA October 31, 2019 07:13
Hi,
I got the same error while running in parallel. Have anybody found a solution for this problem?
Thanks in advanced.


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